CSI-TME: Spatial Isoform Analysis Dashboard

Cytokine & Secreted protein spatial Isoform distribution in the Tumor MicroEnvironment

Analysis Summary

24
Total Visium Samples
(ONT: 11, SR: 13)
32
Genes Analyzed
15
Genes Validated (scRNA)
194
Significant PSI Events

Validation Tier Summary

Validation Tiers:
TIER1_FULL Strong spatial + scRNA validation
TIER2_SPATIAL Reproducible spatial patterns only
TIER3_SCRNA scRNA validation but limited spatial
TIER4_PARTIAL Partial evidence in either modality

Key Findings

VCAN (Versican): Shows near-complete isoform switching (99% ΔPSI) between macrophages and tumor cells. The largest splicing effect in the dataset, validated both spatially (8/13 SR samples significant) and in scRNA-seq (p=1.4e-180).
APP (Amyloid Precursor Protein): Exon 7/8 inclusion varies dramatically between tumor states (MES: 82% vs NPC: 27%). Spatial HSIC-IR significant in 4/7 samples.
CLU (Clusterin): Most reproducible spatial isoform variation, significant in ALL 11 ONT samples (100%) and validated in scRNA-seq with 26 differential events.

Gene-Level Results

Test Statistics: IR=Isoform Ratio (primary), GC=Gene Counts (expression), IC=Isoform Counts (combined)
Gene Tier IR Sig IR p-val GC Sig GC p-val IC Sig scRNA ΔPSI

Gene Details:

Sample-Level Results

Sample ID Platform Spots Genes Tested Genes Significant Best Gene Best p-value

Sample Details:

scRNA-seq Differential Splicing

32,304 cells from glioma scRNA-seq dataset. PSI values quantified by MARVEL.

Event Types:
SE - Skipped Exon (exon included or excluded)
MXE - Mutually Exclusive Exons (one or the other)
A5SS - Alternative 5' Splice Site
A3SS - Alternative 3' Splice Site
AFE - Alternative First Exon
ALE - Alternative Last Exon
Gene Event Type Exon/Region State 1 State 2 PSI 1 PSI 2 ΔPSI padj

Interactive Figure Viewer

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Main Figures: Key results including PSI boxplots and spatial isoform switching patterns.
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Download Data

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Source Files

Original data files in reports/ directory:

  • ont_splisosm_full_results.csv - ONT HSIC-IR results
  • pilot_splisosm_full_results.csv - SR HSIC-IR results
  • scrna_full_psi_differential.csv - All PSI comparisons
  • spacet_isoform_correlations.csv - Cell type correlations
  • final_validation_report.csv - Validation tier summary